Strain identifier

BacDive ID: 14128

Type strain: Yes

Species: Sphingobacterium composti

Strain Designation: 4M24

Strain history: KACC 11313 <-- H.-Y. Weon 4M24.

NCBI tax ID(s): 415956 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7741

BacDive-ID: 14128

DSM-Number: 18850

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Sphingobacterium composti 4M24 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cotton waste compost.

NCBI tax id

  • NCBI tax id: 415956
  • Matching level: species

strain history

@refhistory
7741<- S.-W. Kwon, KACC <- Yoo et al.; 4M24
67770KACC 11313 <-- H.-Y. Weon 4M24.

doi: 10.13145/bacdive14128.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium composti
  • full scientific name: Sphingobacterium composti Yoo et al. 2007

@ref: 7741

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium composti [homonym]

full scientific name: Sphingobacterium composti [homonym] Yoo et al. 2007

strain designation: 4M24

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32089negative1.5 µm0.55 µmrod-shapedno
69480no93.586
69480negative99.995

pigmentation

  • @ref: 32089
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7741
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7741positivegrowth28mesophilic
32089positivegrowth10-45
32089positiveoptimum27.5mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32089positivegrowth06-09alkaliphile
32089positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32089
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32089no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
32089NaClpositivegrowth0-5 %
32089NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3208922599arabinose+carbon source
3208917057cellobiose+carbon source
3208928757fructose+carbon source
3208933984fucose+carbon source
3208928260galactose+carbon source
3208917234glucose+carbon source
3208917716lactose+carbon source
3208917306maltose+carbon source
3208937684mannose+carbon source
3208928053melibiose+carbon source
32089506227N-acetylglucosamine+carbon source
3208916634raffinose+carbon source
3208917814salicin+carbon source
3208917992sucrose+carbon source
3208927082trehalose+carbon source
3208953424tween 20+carbon source
3208953426tween 80+carbon source
3208918222xylose+carbon source

enzymes

@refvalueactivityec
32089acid phosphatase+3.1.3.2
32089alkaline phosphatase+3.1.3.1
32089catalase+1.11.1.6
32089cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7741cotton waste compostRepublic of KoreaKORAsia
67770Cotton-waste compostsRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Biodegradation#Composting
#Engineered#Waste#Solid plant waste
#Host#Plants#Shrub (Scrub)

taxonmaps

  • @ref: 69479
  • File name: preview.99_67864.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_29308;97_36949;98_47815;99_67864&stattab=map
  • Last taxonomy: Sphingobacterium composti subclade
  • 16S sequence: EF122436
  • Sequence Identity:
  • Total samples: 1994
  • soil counts: 427
  • aquatic counts: 360
  • animal counts: 989
  • plant counts: 218

Sequence information

16S sequences

  • @ref: 32089
  • description: Sphingobacterium composti Yoo et al. 2007 strain 4M24 16S ribosomal RNA gene, partial sequence
  • accession: EF122436
  • length: 1487
  • database: nuccore
  • NCBI tax ID: 415956

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 strain DSM 18850415956.3wgspatric415956
66792Sphingobacterium composti DSM 188502700988711draftimg415956
67770Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 DSM 18850GCA_008124885scaffoldncbi415956

GC content

@refGC-contentmethod
3208942.3
6777042.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.133no
anaerobicno98.418yes
halophileno89.819no
spore-formingno96.478no
glucose-utilyes92.25yes
aerobicyes85.525no
flagellatedno95.041yes
motileno91.693yes
thermophileno97.554yes
glucose-fermentno90.549no

External links

@ref: 7741

culture collection no.: DSM 18850, KACC 11313, JCM 16391, NBRC 106383

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625199Sphingobacterium composti sp. nov., isolated from cotton-waste composts.Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64948-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gossypium/microbiology, Korea, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil, *Soil Microbiology, Sphingobacterium/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny18768611Sphingobacterium anhuiense sp. nov., isolated from forest soil.Wei W, Zhou Y, Wang X, Huang X, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.65864-02008Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/physiology, Temperature, *TreesGenetics
Phylogeny24052628Sphingobacterium arenae sp. nov., isolated from sandy soil.Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, Lin M, Zhang W, Luo XInt J Syst Evol Microbiol10.1099/ijs.0.051706-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silicon Dioxide, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25201914Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert.Zhao P, Zhou Z, Chen M, Lin W, Zhang W, Wei GInt J Syst Evol Microbiol10.1099/ijs.0.064246-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7741Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18850)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18850
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32089Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2833528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1